• Bulletin of the Korean Chemical Society
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• v.34 no.11
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• pp.3284-3288
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• 2013

This paper describes first development and validation of pentafluorophenylprophyl ligand-based liquid chromatography coupled to tandem mass spectrometry (PFPLC-MS/MS) method to determine metformin, a highly polar compound, in human plasma. Metformin and Phenformin (internal standard) were extracted from human plasma 50 ${\mu}L$ with a single-step protein precipitation. The chromatographic separation was performed using a linear gradient elution of mobile phase involving 5.0 mM ammonium formate solution with 0.1% formic acid (A) and acetonitrile (B) over 3.0 min of run time on a Phenomenex Luna PFP column. The detection was performed using a triple-quadrupole tandem mass spectrometer (Waters Quattro micro) with electrospray ionization in the mode of positive ionization and multiple-reaction monitoring (MRM). The developed method was validated with 5.0 ng/mL of lower limit of quantification (LLOQ). The calibration curve was linear over 5-3000 ng/mL of the concentration range ($R^2$ > 0.99). The specificity, selectivity, carry-over effect, precision, accuracy and stability of the method met the acceptance criteria. The method developed in this study had had rapidness, simplicity and ruggedness. The reliable method was successfully applied to high throughput analysis of real samples for a practical purpose of a pharmacokinetic study.

• Genomics & Informatics
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• v.14 no.3
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• pp.104-111
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• 2016

Zika virus (ZIKV) is a mosquito borne pathogen, belongs to Flaviviridae family having a positive-sense single-stranded RNA genome, currently known for causing large epidemics in Brazil. Its infection can cause microcephaly, a serious birth defect during pregnancy. The recent outbreak of ZIKV in February 2016 in Brazil realized it as a major health risk, demands an enhanced surveillance and a need to develop novel drugs against ZIKV. Amodiaquine, prochlorperazine, quinacrine, and berberine are few promising drugs approved by Food and Drug Administration against dengue virus which also belong to Flaviviridae family. In this study, we performed molecular docking analysis of these drugs against nonstructural 3 (NS3) protein of ZIKV. The protease activity of NS3 is necessary for viral replication and its prohibition could be considered as a strategy for treatment of ZIKV infection. Amongst these four drugs, berberine has shown highest binding affinity of -5.8 kcal/mol and it is binding around the active site region of the receptor. Based on the properties of berberine, more similar compounds were retrieved from ZINC database and a structure-based virtual screening was carried out by AutoDock Vina in PyRx 0.8. Best 10 novel drug-like compounds were identified and amongst them ZINC53047591 (2-(benzylsulfanyl)-3-cyclohexyl-3H-spiro[benzo[h]quinazoline-5,1'-cyclopentan]-4(6H)-one) was found to interact with NS3 protein with binding energy of -7.1 kcal/mol and formed H-bonds with Ser135 and Asn152 amino acid residues. Observations made in this study may extend an assuring platform for developing anti-viral competitive inhibitors against ZIKV infection.

• Journal of the Institute of Electronics Engineers of Korea TC
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• v.44 no.12
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• pp.54-62
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• 2007

Mobile IPv6 is the representative standard protocol proposed to offer mobility of mobile hosts, but it has drawbacks such as high handover latency and packet loss during handover. To complement these drawbacks, several protocols have been proposed and they can support faster handover than the Mobile IPv6, but there still exists inevitable packet loss during handover in those protocols. In this paper, we propose a new handover procedure of mobile host who has a dual link for minimizing packet loss rate during micro handover to improve mobility capability of Cellular Ethernet system that supports mobility at layer 2. And we derive the superiority of proposed scheme by comparing in terms of packet loss rate, handover latency and throughput of proposed scheme with those of Hierarchical Mobile IPv6 which is the representative IP-layer micro mobility protocol by simulation.

• Molecules and Cells
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• v.40 no.8
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• pp.587-597
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• 2017

MicroRNAs (miRNAs) are essential small RNA molecules that regulate the expression of target mRNAs in plants and animals. Here, we aimed to identify miRNAs and their putative targets in Hibiscus syriacus, the national flower of South Korea. We employed high-throughput sequencing of small RNAs obtained from four different tissues (i.e., leaf, root, flower, and ovary) and identified 33 conserved and 30 novel miRNA families, many of which showed differential tissuespecific expressions. In addition, we computationally predicted novel targets of miRNAs and validated some of them using 5' rapid amplification of cDNA ends analysis. One of the validated novel targets of miR477 was a terpene synthase, the primary gene involved in the formation of disease-resistant terpene metabolites such as sterols and phytoalexins. In addition, a predicted target of conserved miRNAs, miR396, is SHORT VEGETATIVE PHASE, which is involved in flower initiation and is duplicated in H. syriacus. Collectively, this study provides the first reliable draft of the H. syriacus miRNA transcriptome that should constitute a basis for understanding the biological roles of miRNAs in H. syriacus.

• Journal of KIISE:Computer Systems and Theory
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• v.33 no.5
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• pp.267-281
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• 2006

PPI(Protein-Protein Interaction) data has information about the organism has maintained a life with some kind of mechanism. So, it is used in study about cure research back, cause of disease, and new medicine development. This PPI data has been increased by geometric progression because high throughput methods are developed such as Yeast-two-hybrid, Mass spectrometry, and Correlated mRNA expression. So, it is impossible that a person directly manage and analyze PPI data. Fortunately, PPI data is able to abstract the graph which has proteins as nodes, interactions as edges. Consequently, Graph theory plentifully researched from the computer science until now is able to be applied to PPI data successfully. In this paper, we introduce Proteinca(PROTEin INteraction CAbaret) workbench system for easily managing, analyzing and visualizing PPI data. Proteinca assists the user understand PPI data intuitively as visualizing a PPI data in graph and provide various analytical function on graph theory. And Protenica provides a simplified visualization with gravity-rule.

• The KIPS Transactions:PartA
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• v.12A no.2 s.92
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• pp.171-180
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• 2005

In distributed systems data are replicated and stored at several nodes to increase the availability and overall performance. Here Quorum protocol doffing a certain set of replicas required for read/write operation exists for global concurrency control. One of the representative replication Protocols - the Tree Quorum protocol - has a drawback of rapidly growing number of replicas as the level increases, while the Grid protocol requires the same operation cost even without any failure. In this paper, thus, we propose a new replication protocol called hybrid protocol which capitalizes the merits of the existing protocols and solves the problems of them at the same time. The proposed hybrid protocol has very low operation cost in the absence of failure like the tree quorum protocol, and has relatively lower operation cost and higher availability than existing protocols when failure occurs by employing tree architecture as the overall organization while each level of the tree is organized as a row of a grid architecture. It is thus effective to be applied to survival storage system. We conduct cost and availability analysis of the proposed protocol through mathematical modeling, and response time and throughput are compared with those of the Tree Quorum protocol through computer simulation.

• Journal of Microbiology and Biotechnology
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• v.25 no.8
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• pp.1275-1280
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• 2015

Previously, we performed de novo RNA sequencing of Scolopendra subspinipes mutilans using high-throughput sequencing technology and identified several antimicrobial peptide candidates. Among them, a cationic antimicrobial peptide, scolopendrasin VII, was selected based on its physicochemical properties, such as length, charge, and isoelectric point. Here, we assessed the anticancer activities of scolopendrasin VII against U937 and Jurkat leukemia cell lines. The results showed that scolopendrasin VII decreased the viability of the leukemia cells in MTS assays. Furthermore, flow cytometric analysis and acridine orange/ethidium bromide staining revealed that scolopendrasin VII induced necrosis in the leukemia cells. Scolopendrasin VII-induced necrosis was mediated by specific interaction with phosphatidylserine, which is enriched in the membrane of cancer cells. Taken together, these data indicated that scolopendrasin VII induced necrotic cell death in leukemia cells, probably through interaction with phosphatidylserine. The results provide a useful anticancer peptide candidate and an efficient strategy for new anticancer peptide development.

• Journal of Microbiology and Biotechnology
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• v.24 no.3
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• pp.313-323
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• 2014

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coal-mining reclamation areas was suggested.

• Journal of Microbiology and Biotechnology
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• v.30 no.9
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• pp.1355-1366
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• 2020

Sediment bacterial communities are critical to the biogeochemical cycle in river ecosystems, but our understanding of the relationship between sediment bacterial communities and their specific input streams in rivers remains insufficient. In this study, we analyzed the sediment bacterial community structure in a local river receiving discharge of urban domestic sewage by applying Illumina MiSeq high-throughput sequencing. The results showed that the bacterial communities of sediments samples of different pollution types had similar dominant phyla, mainly Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes, but their relative abundances were different. Moreover, there were great differences at the genus level. For example, the genus Bacillus showed statistically significant differences in the hotel site. The clustering of bacterial communities at various sites and the dominant families (i.e., Nocardioidaceae, and Sphingomonadaceae) observed in the residential quarter differed from other sites. This result suggested that environmentally induced species sorting greatly influenced the sediment bacterial community composition. The bacterial co-occurrence patterns showed that the river bacteria had a nonrandom modular structure. Microbial taxonomy from the same module had strong ecological links (such as the nitrogenium cycle and degradation of organic pollutants). Additionally, PICRUSt metabolic inference analysis showed the most important function of river bacterial communities under the influence of different types of domestic sewage was metabolism (e.g., genes related to xenobiotic degradation predominated in residential quarter samples). In general, our results emphasize that the adaptive changes and interactions in the bacterial community structure of river sediment represent responses to different exogenous pollution sources.

• Journal of the Korea Computer Industry Society
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• v.3 no.1
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• pp.85-94
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• 2002

EMRCA(Explicit Max_min Rate Control Algorithm) switch, which has been proposed in the ATM(Asychronous Transfer Mode) standard, controls the ABR(Available Bit Rate) service traffic in the ATM networks. The ABR service class of ATM networks uses a feedback control mechanism to adapt to varying link capacities. The VS/VD(Virtual Source/Virtual Destination) technique offers the possibility to segment the otherwise end-to-end ABR control loop into separate loops. The improved feedback delay and the control of ABR traffic inside closed segments provide a better performance and QoS(Quality of Service) for ABR connections with respect to throughput, delay, and jitter. This paper is study of an ABR VS/VD flow control method. Linear control theory offers the means to derive correct choices of parameters and to assess performance issues, like stability of the system, during the design phase. The performance goals are a high link utilization, fair bandwidth distribution and robust operation in various environments, which are verified by discrete event simulations. The major contribution of this work is the use of linear control theory to model and design an ABR flow control method tailored for the special layout of a VS/VD switch, the simulation shows that this techniques better than conventional method.